All of the flush mount speakers I've ever encountered (lots) install just as easily for retrofit as for new construction. As far as sound quality is concerned, there really is no noticeable difference. If you're going to hide the wires behind the drywall just make sure you use a method where you can find them again later.

Jeff- nice to hear that your house is moving along. I hope to hear more on your progress and decisions. There are many others on the forum right now that need to read these posts. Your home is a great example.
Are you going to use in-wall speakers for most of your house or in-ceiling speakers?
Use a digital camera or a disposable camera to take pictures after your rough-in. Mark the pictures with the dimensuions from two walls. Tired of drilling holes yet?